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  <div class="section" id="overview-of-biodegradation-properties">
<h1>Overview of Biodegradation Properties<a class="headerlink" href="#overview-of-biodegradation-properties" title="Permalink to this headline">¶</a></h1>
<dl class="field-list simple">
<dt class="field-odd">Release</dt>
<dd class="field-odd"><p>2.0</p>
</dd>
<dt class="field-even">Date</dt>
<dd class="field-even"><p>Mar 16, 2020</p>
</dd>
</dl>
<span class="target" id="module-biodeg_properties"></span><div class="section" id="biodegradation-properties-script">
<h2>Biodegradation Properties Script<a class="headerlink" href="#biodegradation-properties-script" title="Permalink to this headline">¶</a></h2>
<p>Create a dictionary of biodegradation properties</p>
<p>This script creates a dictionary of the properties of several hydrocarbons and
chemicals of environmental interest in a global dictionary for use by other
programs that need to know biodegradation properties.</p>
<div class="section" id="parameters">
<h3>Parameters<a class="headerlink" href="#parameters" title="Permalink to this headline">¶</a></h3>
<p>The biodegradation data are stored in <code class="docutils literal notranslate"><span class="pre">./data/BioData.csv</span></code>. Header rows are 
denoted by <cite>%, the last row of pure text is taken as the variable names and
the last row with `()</cite> is taken as the units.  The columns should include
a key name (e.g., <cite>methane</cite>), the first-order decay constant, and the 
biodegrdation lag time.  For unknown parameter values, use -9999.</p>
<p>For the data provided by the model, the data sources and more details are
documented in the file <code class="docutils literal notranslate"><span class="pre">../docs/BioData_ReadMe.txt</span></code>.</p>
<p>This module can read in any number of columns of chemical data, including
parameters not listed below. Units will be converted to standard SI units,
and the conversion function will operate on 1/d and d. The returned variables
<cite>units</cite> will contain the final set of units for the database. To use the
TAMOC suite of models, all parameters listed below in the <cite>data</cite> dictionary
must be provided with the variable names listed.</p>
</div>
<div class="section" id="returns">
<h3>Returns<a class="headerlink" href="#returns" title="Permalink to this headline">¶</a></h3>
<dl>
<dt>data<span class="classifier">dict</span></dt><dd><p>a nested dictionary containing the chemical name as the first key 
and the following list of secondary keys matched with the numerical
value of each variable:</p>
<blockquote>
<div><p>k_bio : first-order biodegradation rate constant (1/s)
t_bio : biodegradation lag time (s)</p>
</div></blockquote>
</dd>
<dt>units<span class="classifier">dict</span></dt><dd><p>dictionary with the same keys as the variable names listed above 
(e.g., k_bio, t_bio, etc.) linked to a string containing the units of 
each variable.</p>
</dd>
</dl>
</div>
<div class="section" id="notes">
<h3>Notes<a class="headerlink" href="#notes" title="Permalink to this headline">¶</a></h3>
<p>To use the properties database distributed by TAMOC, simply import this file
in Python: the results will be returned in <cite>biodeg_properties.data</cite>. To
import a user-defined database of properties, use the function <code class="docutils literal notranslate"><span class="pre">load_data</span></code>
provided in the <cite>chemical_properties</cite> module. The <code class="docutils literal notranslate"><span class="pre">TAMOC</span></code> suite of models
will pull data from both the default and any user-specified database, giving
first priority to parameter keys found in the user-specified database.</p>
</div>
<div class="section" id="see-also">
<h3>See also<a class="headerlink" href="#see-also" title="Permalink to this headline">¶</a></h3>
<p><cite>dbm</cite> : Uses these dictionaries to create chemical mixture objects.</p>
</div>
<div class="section" id="examples">
<h3>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h3>
<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">tamoc</span> <span class="kn">import</span> <span class="n">biodeg_properties</span> <span class="k">as</span> <span class="n">biodeg</span>
<span class="gp">&gt;&gt;&gt; </span><span class="n">biodeg</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="s1">&#39;methane&#39;</span><span class="p">][</span><span class="s1">&#39;k_bio&#39;</span><span class="p">]</span>
<span class="go">x.xxxxx</span>
<span class="gp">&gt;&gt;&gt; </span><span class="n">biodeg</span><span class="o">.</span><span class="n">units</span><span class="p">[</span><span class="s1">&#39;k_bio&#39;</span><span class="p">]</span>
<span class="go">&#39;(1/s)&#39;</span>
</pre></div>
</div>
</div>
</div>
<div class="section" id="module-functions">
<h2>Module Functions<a class="headerlink" href="#module-functions" title="Permalink to this headline">¶</a></h2>
<table class="longtable docutils align-default">
<colgroup>
<col style="width: 10%" />
<col style="width: 90%" />
</colgroup>
<tbody>
<tr class="row-odd"><td><p><a class="reference internal" href="../autodoc/chem/biodeg_properties.load_data.html#biodeg_properties.load_data" title="biodeg_properties.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>(fname)</p></td>
<td><p>Load a chemical properties file into memory</p></td>
</tr>
</tbody>
</table>
</div>
<div class="section" id="input-data-documentation">
<h2>Input Data Documentation<a class="headerlink" href="#input-data-documentation" title="Permalink to this headline">¶</a></h2>
<p>This script loads the biodegradation properties database into the name space.
If the import command is:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">biodeg_properties</span>
</pre></div>
</div>
<p>then the database is in the <code class="docutils literal notranslate"><span class="pre">biodeg_properties</span></code> namespace.  The <code class="docutils literal notranslate"><span class="pre">TAMOC</span></code>
package usually imports using:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">chemical_properties</span> <span class="k">as</span> <span class="nn">biodeg</span>
</pre></div>
</div>
<p>so that the database is in the <code class="docutils literal notranslate"><span class="pre">biodeg</span></code> namespace.</p>
<p>The data loaded into these namespaces is stored in the file:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="o">./</span><span class="n">data</span><span class="o">/</span><span class="n">BioData</span><span class="o">.</span><span class="n">csv</span>
</pre></div>
</div>
<p>The format for these data is described in</p>
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="bio_data.html">Sources of Data in BioData.csv</a></li>
</ul>
</div>
</div>
</div>


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